BIOL4800/6220_Fall2022_RTutorial

R Basic

Introduction

R as a calculator

1 + 100

2^2

7/2

4-1

2*2

3+5*2

(3+5)*2

2e2

2/10000

sin(1)

log(1)

exp(0)

1 == 1

1 >= 1

1 < 1

1 != 2

x <- 10
x

x + x

x - 5

x^2

y <- x + x
y

Vectorization

1:5

2^(1:5)

v <- 1:5
2^v

log10(v)

Environment

ls()

rm(v)
ls()

Package Management

installed.packages()

#install.packages("vegan", dependencies = TRUE) #Already installed

library(vegan)

#remove.packages()

Project Management

1. Set up management structure (i.e., “data”, “src”, “results”, “doc”)
2. Discuss avoiding redundancy of files
3. Make sure to use version control (i.e., Git)

Getting Help

?plot

help(plot)

?"<-"

vignette("FAQ-vegan")

citation("vegan")

To cite package ‘vegan’ in publications use:

  Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R.
  Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs and Helene Wagner
  (2020). vegan: Community Ecology Package. R package version 2.5-7. https://CRAN.R-project.org/package=vegan

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {vegan: Community Ecology Package},
    author = {Jari Oksanen and F. Guillaume Blanchet and Michael Friendly and Roeland Kindt and Pierre Legendre and Dan McGlinn and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner},
    year = {2020},
    note = {R package version 2.5-7},
    url = {https://CRAN.R-project.org/package=vegan},
  }

ATTENTION: This citation information has been auto-generated from the package DESCRIPTION file and may need
manual editing, see ‘help("citation")’.

Data and their formats

cats <- data.frame(coat = c("calico", "black", "tabby"),
                   weight = c(2.1,5,3.2),
                   likes_string = c(1,0,1))

write.csv(cats, file = "~/GitHub/biol48006220_Fall2022/practcomp_2022/data/cats.csv")

cats$coat

[1] "calico" "black"  "tabby" 

cats$weight

[1] 2.1 5.0 3.2

cats$weight*10

[1] 21 50 32

log(cats$weight)

[1] 0.7419373 1.6094379 1.1631508

cats <- cbind(cats, logweight)

paste("My cat is ", cats$coat, ", and it weighs ", cats$weight, " kg.", sep = "")

[1] "My cat is calico, and it weighs 2.1 kg." "My cat is black, and it weighs 5 kg."   
[3] "My cat is tabby, and it weighs 3.2 kg." 

Data Types

typeof(cats$coat)

[1] "character"

typeof(cats$weight)

[1] "double"

typeof(cats$likes_string)

[1] "double"

typeof(3.14159)

[1] "double"

typeof(1i)

[1] "complex"

typeof(FALSE)

[1] "logical"

typeof(T)

[1] "logical"

typeof(cats)

[1] "list"

class(cats)

[1] "data.frame"

file.show("./data/cats.csv")

typeof(cats$likes_string)

[1] "logical"

cats$likes_string

[1]  TRUE FALSE  TRUE

c("a", "b")

[1] "a" "b"

ab

[1] "a" "b"

c(ab, "c")

[1] "a" "b" "c"

c(ab, ab)

[1] "a" "b" "a" "b"

1:10

 [1]  1  2  3  4  5  6  7  8  9 10

seq(10)

 [1]  1  2  3  4  5  6  7  8  9 10

head(z, n=3)

[1] 1 2 3

length(z)

[1] 10

class(z)

[1] "integer"

typeof(z)

[1] "integer"

seq(0,100, by=5)

 [1]   0   5  10  15  20  25  30  35  40  45  50  55  60  65  70  75  80  85  90  95 100

Data Frames

str(cats$coat)

 chr [1:3] "calico" "black" "tabby"

coats

[1] "tabby"         "tortoiseshell" "tortoiseshell" "black"         "tabby"        

str(coats)

 chr [1:5] "tabby" "tortoiseshell" "tortoiseshell" "black" "tabby"

factor(coats)

[1] tabby         tortoiseshell tortoiseshell black         tabby        
Levels: black tabby tortoiseshell

class(categories)

[1] "factor"

str(categories)

 Factor w/ 3 levels "black","tabby",..: 2 3 3 1 2

Lists

list_example <- list(title="Numbers", numbers = 1:10, data=T)

list_example

$title
[1] "Numbers"

$numbers
 [1]  1  2  3  4  5  6  7  8  9 10

$data
[1] TRUE

another_list

[[1]]
[1] 1

[[2]]
[1] "a"

[[3]]
[1] TRUE

[[4]]
[1] 1+1i

class(list_example)

[1] "list"

class(cats)

[1] "data.frame"

Matrices

# By definition, matrices are all numbers

matrix_example <- matrix(0, ncol = 5, nrow = 3)

matrix_example

class(matrix_example)

typeof(matrix_example)

str(matrix_example)

dim(matrix_example)

ncol(matrix_example)
nrow(matrix_example)

class(data.frame(matrix_example))

df_example <- data.frame(matrix_example)
df_example

Subsetting

p <- c(2.3, 6.9, 4.0, 23, 1)
p

names(p) <- c('a', 'b', 'c', 'd', 'e')
p

p[1]

p[2:4]

p[c(1,5)]

p[c(1,1,1,3,5,5)]

p[6]

p[-3]

p[c(-1,-5)]

p[-(2:4)]

p[c('a','c')]

p[c(T,F,T,F,T)]

p[names(p) != 'c']

Factors

f <- factor(c('a','b','c','d','e'))
f

f[f=='a']

f[1:3]

f[f %in% c('b','c')]

f[-3]

f2 <- factor(c('a','a','d','c','c'))
f2

f2[f2 == 'a']

f2[f2 %in% c('a','c')]

Matrices Resumed

m

           [,1]       [,2]       [,3]        [,4]
[1,] -1.1968205 -0.3943568  0.4232027 -2.34367583
[2,] -0.9516674 -1.2484030 -1.8461725 -0.77605977
[3,]  0.2786364 -0.6521289 -0.2456747 -2.16173144
[4,] -1.4449411 -1.1707346  1.2538299  0.05701057
[5,]  0.8216518  0.3604497  1.5633419 -0.24867199
[6,]  1.2470188  1.2302708 -1.2644661 -0.07830796

m[,c(3,4)]

           [,1]        [,2]
[1,]  0.4232027 -2.34367583
[2,] -1.8461725 -0.77605977
[3,] -0.2456747 -2.16173144
[4,]  1.2538299  0.05701057
[5,]  1.5633419 -0.24867199
[6,] -1.2644661 -0.07830796

Lists Revisted

xlist

$a
[1] "BIOL48006220"

$b
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0

$data
[1] "Grade"

xlist[1:2]

$a
[1] "BIOL48006220"

$b
 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0

xlist['a']

$a
[1] "BIOL48006220"

xlist[['a']]

[1] "BIOL48006220"

xlist[['b']]

 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0

xlist$b

 [1]  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0

Data Frames Revisted

gp <- read.csv("/Users/colinfinlay/GitHub/biol48006220_Fall2022/practcomp_2022/data/forest_area_sq_km.numbers")

Warning: line 1 appears to contain embedded nullsWarning: line 3 appears to contain embedded nullsWarning: line 4 appears to contain embedded nullsWarning: line 5 appears to contain embedded nullsWarning: EOF within quoted stringWarning: embedded nul(s) found in input

head(gp, n=10L)

Warning messages:
1: replacing previous import ‘lifecycle::last_warnings’ by ‘rlang::last_warnings’ when loading ‘tibble’ 
2: replacing previous import ‘lifecycle::last_warnings’ by ‘rlang::last_warnings’ when loading ‘pillar’ 

nrow(gp)

[1] 214

head(gp[["country"]], 10L)

 [1] "Aruba"                "Afghanistan"          "Angola"               "Albania"              "Andorra"             
 [6] "United Arab Emirates" "Argentina"            "Armenia"              "American Samoa"       "Antigua and Barbuda" 

gp$X2001

  [1] "4.2"   "12.1k" "766k"  "7720"  "160"   "3110"  "327k"  "3320"  "177"   "93.2"  "1.31M" "38.4k" "9960"  "1940"  "6720" 
 [16] "40.4k" "71.2k" "19.1k" "34.5k" "4"     "5100"  "21.1k" "83.4k" "14.5k" "10"    "547k"  "5.43M" "63"    "3940"  "26.3k"
 [31] "174k"  "228k"  "3.48M" "8.68"  "12k"   "160k"  "1.82M" "48.7k" "215k"  "1.43M" "222k"  "623k"  "408"   "403"   "28.6k"
 [46] "25.3k" "129"   "1720"  "26.4k" "114k"  "56"    "479"   "5750"  "19.9k" "16.5k" "136k"  "605"   "11.1k" "174k"  "22.6k"
 [61] "184k"  "224k"  "10.2k" "155k"  "0.8"   "639"   "237k"  "34.6"  "29.8k" "27.7k" "86.7k" "0"     "68.6k" "3460"  "21.3k"
 [76] "26k"   "36.6k" "177"   "2.2"   "41.1k" "240"   "186k"  "67.4k" "18.9k" "3800"  "19.5k" "1.01M" "680k"  "6480"  "96k"  
 [91] "8190"  "328"   "1530"  "85k"   "5280"  "975"   "249k"  "31.4k" "38.9k" "11.9k" "107k"  "11.8"  "110"   "64.6k" "51.3" 
[106] "173k"  "1380"  "81.6k" "2170"  "210"   "67"    "21.5k" "345"   "20.5k" "871"   "32.7k" "10"    "55.4k" "0"     "3500" 
[121] "129k"  "8.2"   "681k"  "94"    "9580"  "133k"  "3.5"   "342k"  "6260"  "142k"  "316"   "407k"  "4110"  "412"   "30k"  
[136] "195k"  "79.2k" "8380"  "13k"   "246k"  "51.6k" "3620"  ""      "121k"  "58.2k" "0"     "98.5k" "30"    "44.3k" "44.2k"
[151] "750k"  "72.2k" "398"   "363k"  "91.1k" "4420"  "64.1k" "32.8k" "223k"  "91.2"  "1490"  "0"     "64k"   "8.1M"  "2830" 
[166] "9770"  ""      "87.8k" "172"   "25.4k" "28.9k" "6650"  "10"    "73.6k" "24.8k" ""      "583"   "153k"  "19k"   "12.4k"
[181] "281k"  "4760"  ""      "337"   "4440"  "105"   "61.9k" "12.6k" "192k"  "4100"  "41.3k" "9460"  "89.5"  "2360"  "6720" 
[196] "203k"  "10"    "529k"  "30.8k" "95.2k" "14.4k" "3.05M" "30.4k" "285"   "488k"  "36.6"  "201"   "121k"  "4420"  "1700" 
[211] "5490"  "177k"  "470k"  "183k" 

Conditionals and Flow

if (n<10) {
  print("n is less than 10")
} else if (n>10) {
  print("n is greater than 10")
} else {
  print("n is equal to 10")
}

[1] "n is equal to 10"

for (n in seq(1,20)) {
  if (n<10) {
    print("n is less than 10")
  } else if (n>10) {
    print("n is greater than 10")
  } else {
   print("n is equal to 10")
  }
}

[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is less than 10"
[1] "n is equal to 10"
[1] "n is greater than 10"
[1] "n is greater than 10"
[1] "n is greater than 10"
[1] "n is greater than 10"
[1] "n is greater than 10"
[1] "n is greater than 10"
[1] "n is greater than 10"
[1] "n is greater than 10"
[1] "n is greater than 10"
[1] "n is greater than 10"

while (g <=10) {
  print(paste(g, "is less than or equal to 10"))
  g <- g+1
}

[1] "0 is less than or equal to 10"
[1] "1 is less than or equal to 10"
[1] "2 is less than or equal to 10"
[1] "3 is less than or equal to 10"
[1] "4 is less than or equal to 10"
[1] "5 is less than or equal to 10"
[1] "6 is less than or equal to 10"
[1] "7 is less than or equal to 10"
[1] "8 is less than or equal to 10"
[1] "9 is less than or equal to 10"
[1] "10 is less than or equal to 10"

Plotting

library(ggplot2)

africas <- gapminder[gapminder$continent=="Africa", ]

ggplot(data=africas, mapping = aes(x=year, y=lifeExp)) +
  geom_line() +
  facet_wrap(~country) +
  theme(axis.text.x = element_text(angle = 90)) +
  labs(
    x = "Year",
    y = "Life Expectancy",
    title = "Life Expectancy Over Time in African Countries"
  )

ggsave(filename = "./data/AfricanLifeExp.png", plot = AfricanLifeExp, width = 24, height = 40, dpi = 300, units = "cm")

Error in grDevices::dev.off() : 
  QuartzBitmap_Output - unable to open file './data/AfricanLifeExp.png'

pdf(file = "/Users/colinfinlay/GitHub/biol48006220_Fall2022/practcomp_2022/results/AfricanLifeExp.pdf", width = 24, height = 40)
plot(AfricanLifeExp)
dev.off()

null device 
          1 

write.table(gapminder, file="/data/gapminder_web.csv", sep = ",")

Warning: cannot open file '/data/gapminder_web.csv': No such file or directoryError in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection

write.csv(africas, file="/Users/colinfinlay/GitHub/biol48006220_Fall2022/practcomp_2022/data/gapminder_web_africas.csv")

Fancy Plots

install.packages(c("ggridges", "viridis", "hrbrthemes"), dependencies = T)

also installing the dependencies ‘deldir’, ‘lazyeval’, ‘png’, ‘jpeg’, ‘interp’, ‘rex’, ‘sp’, ‘terra’, ‘latticeExtra’, ‘systemfonts’, ‘extrafontdb’, ‘Rttf2pt1’, ‘covr’, ‘patchwork’, ‘ggplot2movies’, ‘vdiffr’, ‘hexbin’, ‘dichromat’, ‘raster’, ‘rasterVis’, ‘mapproj’, ‘svglite’, ‘rgdal’, ‘maps’, ‘extrafont’, ‘gdtools’, ‘hunspell’, ‘gcookbook’

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hrbrthemes::import_roboto_condensed()

sh: line 1:  1576 Segmentation fault: 11  '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/hrbrthemes/fonts/roboto-condensed/RobotoCondensed-Bold.ttf' '/var/folders/r1/3zp0c6w516g61fbl6pqcz7gr0000gn/T//RtmpKhjam5/fonts/RobotoCondensed-Bold' 2>&1
sh: line 1:  1578 Segmentation fault: 11  '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/hrbrthemes/fonts/roboto-condensed/RobotoCondensed-Light.ttf' '/var/folders/r1/3zp0c6w516g61fbl6pqcz7gr0000gn/T//RtmpKhjam5/fonts/RobotoCondensed-Light' 2>&1
sh: line 1:  1580 Segmentation fault: 11  '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rttf2pt1/exec//ttf2pt1' -a -GfAe '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/hrbrthemes/fonts/roboto-condensed/RobotoCondensed-Regular.ttf' '/var/folders/r1/3zp0c6w516g61fbl6pqcz7gr0000gn/T//RtmpKhjam5/fonts/RobotoCondensed-Regular' 2>&1
You will likely need to install these fonts on your system as well.

You can find them in [/Library/Frameworks/R.framework/Versions/4.2/Resources/library/hrbrthemes/fonts/roboto-condensed]

Statistics

install.packages(c("ggstatsplot", "palmerpenguins"), dependencies = T)

also installing the dependencies ‘listenv’, ‘parallelly’, ‘future’, ‘globals’, ‘future.apply’, ‘progressr’, ‘SQUAREM’, ‘checkmate’, ‘matrixStats’, ‘RcppGSL’, ‘lava’, ‘elliptic’, ‘contfrac’, ‘deSolve’, ‘Brobdingnag’, ‘inline’, ‘loo’, ‘pkgbuild’, ‘bdsmatrix’, ‘RcppZiggurat’, ‘iterators’, ‘rngtools’, ‘prodlim’, ‘bayestestR’, ‘prismatic’, ‘effectsize’, ‘zeallot’, ‘lmerTest’, ‘coda’, ‘hypergeo’, ‘bridgesampling’, ‘LaplacesDemon’, ‘logspline’, ‘RcppParallel’, ‘rstan’, ‘rstantools’, ‘BH’, ‘StanHeaders’, ‘metadat’, ‘mathjaxr’, ‘bbmle’, ‘fastGHQuad’, ‘Rfast’, ‘doParallel’, ‘foreach’, ‘doRNG’, ‘gmp’, ‘Rmpfr’, ‘SuppDists’, ‘kSamples’, ‘BWStest’, ‘mnormt’, ‘commonmark’, ‘reshape’, ‘mc2d’, ‘gower’, ‘hardhat’, ‘ipred’, ‘timeDate’, ‘correlation’, ‘datawizard’, ‘insight’, ‘paletteer’, ‘parameters’, ‘performance’, ‘statsExpressions’, ‘afex’, ‘BayesFactor’, ‘gapminder’, ‘ggcorrplot’, ‘ggside’, ‘metaBMA’, ‘metafor’, ‘metaplus’, ‘PMCMRplus’, ‘psych’, ‘spelling’, ‘WRS2’, ‘recipes’

  There is a binary version available but the source version is later:

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/listenv_0.8.0.tgz'
Content type 'application/x-gzip' length 103223 bytes (100 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/parallelly_1.32.1.tgz'
Content type 'application/x-gzip' length 302748 bytes (295 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/future_1.28.0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/globals_0.16.1.tgz'
Content type 'application/x-gzip' length 106135 bytes (103 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/future.apply_1.9.1.tgz'
Content type 'application/x-gzip' length 151535 bytes (147 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/progressr_0.11.0.tgz'
Content type 'application/x-gzip' length 272289 bytes (265 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/SQUAREM_2021.1.tgz'
Content type 'application/x-gzip' length 176568 bytes (172 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/checkmate_2.1.0.tgz'
Content type 'application/x-gzip' length 694554 bytes (678 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/matrixStats_0.62.0.tgz'
Content type 'application/x-gzip' length 590827 bytes (576 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/RcppGSL_0.3.11.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/elliptic_1.4-0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/contfrac_1.1-12.tgz'
Content type 'application/x-gzip' length 27492 bytes (26 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/deSolve_1.34.tgz'
Content type 'application/x-gzip' length 2619125 bytes (2.5 MB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/Brobdingnag_1.2-9.tgz'
Content type 'application/x-gzip' length 1325577 bytes (1.3 MB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/inline_0.3.19.tgz'
Content type 'application/x-gzip' length 127274 bytes (124 KB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/loo_2.5.1.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/pkgbuild_1.3.1.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/bdsmatrix_1.3-6.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/RcppZiggurat_0.1.6.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/iterators_1.0.14.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/rngtools_1.5.2.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/prodlim_2019.11.13.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/bayestestR_0.13.0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/prismatic_1.1.1.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/effectsize_0.8.1.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/zeallot_0.1.0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/lmerTest_3.1-3.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/coda_0.19-4.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/hypergeo_1.2-13.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/bridgesampling_1.1-2.tgz'
Content type 'application/x-gzip' length 1723346 bytes (1.6 MB)
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/LaplacesDemon_16.1.6.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/logspline_2.1.17.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/RcppParallel_5.1.5.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/rstantools_2.2.0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/BH_1.78.0-0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/StanHeaders_2.21.0-7.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/metadat_1.2-0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/mathjaxr_1.6-0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/bbmle_1.0.25.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/fastGHQuad_1.0.1.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/Rfast_2.0.6.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/doParallel_1.0.17.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/foreach_1.5.2.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/doRNG_1.8.2.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/gmp_0.6-6.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/Rmpfr_0.8-9.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/SuppDists_1.1-9.7.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/kSamples_1.2-9.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/BWStest_0.2.2.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/mnormt_2.1.1.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/commonmark_1.8.1.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/reshape_0.8.9.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/mc2d_0.1-21.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/hardhat_1.2.0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ipred_0.9-13.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/timeDate_4021.106.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/correlation_0.8.3.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/datawizard_0.6.3.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/insight_0.18.6.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/paletteer_1.5.0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/BayesFactor_0.9.12-4.4.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/gapminder_0.3.0.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/metaplus_1.0-4.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/psych_2.2.9.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/spelling_2.2.tgz'
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trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/palmerpenguins_0.1.1.tgz'
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The downloaded binary packages are in
    /var/folders/r1/3zp0c6w516g61fbl6pqcz7gr0000gn/T//RtmpKhjam5/downloaded_packages

installing the source package ‘lava’

trying URL 'https://cran.rstudio.com/src/contrib/lava_1.7.0.tar.gz'
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* installing *source* package ‘lava’ ...
** package ‘lava’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lava)

The downloaded source packages are in
    ‘/private/var/folders/r1/3zp0c6w516g61fbl6pqcz7gr0000gn/T/RtmpKhjam5/downloaded_packages’

5. summary

summary()

5. plot

1. Histograms

hist(cats, breaks = "scott")

Error in hist.default(cats, breaks = "scott") : 'x' must be numeric

hist(pedes, breaks= "scott", prob = T)
lines(density(pedes))

Bivariate and Multivariate Statistics

1. Plotting and Regression

1. Box plotting